Dear Steve, Users,
I have a quick question. If we switch on the special bonds for 1-2, 1-3 1-4 interactions (for non-bonded case), does it affect the bonded interactions or are these on the top of bonded interactions? I ran some test simulations with different factors for 1-2,1-3 and 1-4 interactions and the bond and angle energies did not change at all, although the overall vdwl energy got modified.
Regards,
Vikas